Heres how I would code what you have already:

#!/usr/bin/perl

use strict;
use warnings;
#use BeginPerlBioinfo;

srand($$|time);

my $data = {
    'Homo Sapien' => {
        Chromosomes => {
            (map { $_ => {Contigs => 25} } (1..22, qw/X Y/)), # Auto g
+en
            1 => {Contigs => 30},   # Override these two..
            2 => {Contigs => 28},
        },
    },
};

# This program will download the sequences from a given organism
my $organism = ask('Which organism would you like to download the '.
                    'sequences from?');
#my $organism = 'Homo Sapien';

my $number = ask("How many sequences do you want to generate?");
#my $number = 10;

if (exists $data->{$organism})
{
    for (1..$number)
    {
        my $chromosome = random_element(keys%{$data->{$organism}{Chrom
+osomes}});
        print " Chromosome '$chromosome' \n";
        
        my $contig = random_element( 
                     (1..$data->{$organism}{Chromosomes}{$chromosome}{
+Contigs})
        );
        print " Contig '$contig' \n";
    }
}
else
{
    print "I don't know anything about organism: '$organism'\n";
}

exit;

################
#
##############

# ask
#
# Sub which asks a given question and returns the chomped input from t
+he user

sub ask {
    my $query = shift;
    print $query, ":\n";
    my $answer = <STDIN>;
    chomp $answer;
    return $answer;
}

# random_element
#
# Sub routine that picks up random element from a given array

sub random_element{
    # I think there's a problem with the randomness of this
    return $_[int rand(0+@_)]; 
}
[download]

That was really helpful. I am looking into the matter now. Thank you for your help.
Sameet